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UCT CBIO

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  1. proteomics-pipelines proteomics-pipelines Public

    A repo with a proteogenomics and metaproteomics pipeline developed by Matthys Potgieter.

    Jupyter Notebook 9 4

  2. 16S-rDNA-pipeline 16S-rDNA-pipeline Public

    This repository contains an older version of our 16S rDNA diversity analysis pipeline. It uses a combination of bash scripts. To get a more updated version of the pipeline using Nextflow please go …

    R 2 3

  3. 16S-rDNA-dada2-pipeline 16S-rDNA-dada2-pipeline Public

    Forked from HPCBio/16S-rDNA-dada2-pipeline

    dada2 Nextflow pipeline

    Nextflow 2 5

  4. bacterial_variant_calling bacterial_variant_calling Public

    A pipeline for variant calling on bacterial genomes created with Nextflow and singularity / docker

    Nextflow 1 4

  5. ngs-academy ngs-academy Public

    JavaScript 1 1

  6. bst-sysadmin bst-sysadmin Public

    Scripts for maintaining services and setup on the bst.cbio.uct.ac.za server. Also contain some scripts to pull info from the BST Redmine instance.

    Shell

Repositories

Showing 10 of 13 repositories
  • ngs-academy Public
    uct-cbio/ngs-academy’s past year of commit activity
    JavaScript 1 1 0 0 Updated Jan 17, 2025
  • proteomics-pipelines Public

    A repo with a proteogenomics and metaproteomics pipeline developed by Matthys Potgieter.

    uct-cbio/proteomics-pipelines’s past year of commit activity
    Jupyter Notebook 9 MIT 4 0 7 Updated Dec 31, 2024
  • bacterial_variant_calling Public

    A pipeline for variant calling on bacterial genomes created with Nextflow and singularity / docker

    uct-cbio/bacterial_variant_calling’s past year of commit activity
    Nextflow 1 MIT 4 2 1 Updated Jul 24, 2023
  • bst-sysadmin Public

    Scripts for maintaining services and setup on the bst.cbio.uct.ac.za server. Also contain some scripts to pull info from the BST Redmine instance.

    uct-cbio/bst-sysadmin’s past year of commit activity
    Shell 0 MIT 0 0 0 Updated Jul 5, 2021
  • software-demo Public

    Testing github for hosting releases of in-house software

    uct-cbio/software-demo’s past year of commit activity
    HTML 0 MIT 0 0 0 Updated Dec 22, 2020
  • RNAseq-pipeline Public Forked from nf-core/rnaseq

    RNA sequencing analysis pipeline using STAR or HISAT2, with gene counts and quality control

    uct-cbio/RNAseq-pipeline’s past year of commit activity
    Nextflow 0 MIT 720 0 0 Updated Feb 12, 2020
  • 16S-rDNA-pipeline Public

    This repository contains an older version of our 16S rDNA diversity analysis pipeline. It uses a combination of bash scripts. To get a more updated version of the pipeline using Nextflow please go here: https://github.com/h3abionet/h3abionet16S/tree/master/workflows-nxf

    uct-cbio/16S-rDNA-pipeline’s past year of commit activity
    R 2 MIT 3 0 0 Updated Nov 27, 2019
  • varscan Public Forked from dkoboldt/varscan

    Variant calling and somatic mutation/CNV detection for next-generation sequencing data

    uct-cbio/varscan’s past year of commit activity
    0 34 0 0 Updated Jul 25, 2019
  • 16S-rDNA-dada2-pipeline Public Forked from HPCBio/16S-rDNA-dada2-pipeline

    dada2 Nextflow pipeline

    uct-cbio/16S-rDNA-dada2-pipeline’s past year of commit activity
    Nextflow 2 MIT 20 0 0 Updated May 31, 2019
  • uct-srst2 Public Forked from kviljoen/uct-srst2

    MLST using srst2, implemented in Nextflow

    uct-cbio/uct-srst2’s past year of commit activity
    Nextflow 0 GPL-3.0 3 0 0 Updated May 22, 2019
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